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- PDB-1ebg: CHELATION OF SER 39 TO MG2+ LATCHES A GATE AT THE ACTIVE SITE OF ... -

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Basic information

Entry
Database: PDB / ID: 1ebg
TitleCHELATION OF SER 39 TO MG2+ LATCHES A GATE AT THE ACTIVE SITE OF ENOLASE: STRUCTURE OF THE BIS(MG2+) COMPLEX OF YEAST ENOLASE AND THE INTERMEDIATE ANALOG PHOSPHONOACETOHYDROXAMATE AT 2.1 ANGSTROMS RESOLUTION
ComponentsENOLASE
KeywordsCARBON-OXYGEN LYASE
Function / homology
Function and homology information


Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding ...Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHONOACETOHYDROXAMIC ACID / Enolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWedekind, J.E. / Reed, G.H. / Rayment, I.
CitationJournal: Biochemistry / Year: 1994
Title: Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution.
Authors: Wedekind, J.E. / Poyner, R.R. / Reed, G.H. / Rayment, I.
History
DepositionApr 27, 1994Processing site: BNL
Revision 1.0Apr 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8738
Polymers93,4662
Non-polymers4076
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-57 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.500, 73.900, 94.800
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 143 / 2: CIS PROLINE - PRO B 143
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.63425, 0.68696, -0.35469), (0.68803, 0.29229, -0.66421), (-0.35262, -0.66532, -0.65804)
Vector: 61.48104, -8.33861, 47.3677)
DetailsTHE TRANSFORMATION PRESENTED IN *MTRIX* RECORDS BELOW PLACES SUBUNIT II (RESIDUES B 1 - B 436) ONTO SUBUNIT I BY A TWO-FOLD OPERATION AND TRANSLATION THAT DESCRIBE THE NON-CRYSTALLOGRAPHIC DYAD. (CARTESIAN COORDINATE SYSTEM). THE RESULTS ARE GOOD TO ONLY THREE SIGNIFICANT FIGURES. THE CRYSTALLOGRAPHICALLY INDEPENDENT UNIT IS ONE DIMER OF CHEMICALLY IDENTICAL SUBUNITS.

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Components

#1: Protein ENOLASE


Mass: 46732.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00924, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PAH / PHOSPHONOACETOHYDROXAMIC ACID


Mass: 155.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROLINE 143 AND 265 WERE OBSERVED AS CIS IN PREVIOUS STRUCTURES 3ENL THROUGH 7ENL. PROLINE 265 ...PROLINE 143 AND 265 WERE OBSERVED AS CIS IN PREVIOUS STRUCTURES 3ENL THROUGH 7ENL. PROLINE 265 APPEARS TRANS IN THIS STRUCTURE.
Nonpolymer detailsPHOSPHONOACETOHYDROXAMATE WAS CO-CRYSTALLIZED WITH THE ENZYME IN THE PRESENCE OF MG2+. BOTH METALS ...PHOSPHONOACETOHYDROXAMATE WAS CO-CRYSTALLIZED WITH THE ENZYME IN THE PRESENCE OF MG2+. BOTH METALS ARE HEXACOORDINATE WITH OCTAHEDRAL GEOMETRY. IN MUCH OF THE PREVIOUS LITERATURE ON ENOLASE, THE METAL ION WHICH BINDS TIGHTLY TO ENOLASE IN THE ABSENCE OF SUBSTRATES HAS BEEN CALLED THE "CONFORMATIONAL" METAL. THE SECOND METAL ION WHICH BINDS TO ENOLASE IN THE PRESENCE OF THE SUBSTRATE HAS BEEN CALLED THE "CATALYTIC" METAL ION. THE AUTHORS WILL REFER TO THE TWO DIVALENT CATIONS IN ORDER OF DECREASING BINDING AFFINITY AS METAL I AND METAL II, RESPECTIVELY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growDetails: CRYSTALS WERE GROWN FROM POLYETHYLENE GLYCOL, KCE, AT PH 8.2.
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
132 %(w/w)PEG800011
20.5 M11KCl
380 mMHEPPS-NaOH11

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 100 Å / Num. obs: 38673 / % possible obs: 77 % / Num. measured all: 84862 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.21 Å / % possible obs: 40 % / Num. unique obs: 2799 / Num. measured obs: 2805 / Rmerge(I) obs: 0.166

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
RefinementRfactor obs: 0.186 / Highest resolution: 2.1 Å / σ(F): 0
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 22 354 6960
Software
*PLUS
Name: AMORE/TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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